My jeep is still a work in progress, but you should be able to get an idea of how yours will look... I cannot recall if mine are Smittybilt or TAG, but the flares are very similar. This is a 94 YJ with 4" suspension lift and 31 x 9.5" tires.

The flares I purchased came with Phillips head screws. Each screw fit into a small cup a little bigger than the screw head and had a plastic cap that snapped over the screw head once the flare was attached. I had a problem with the caps popping off.

To address this, I purchased some stainless steel 5/16" sheet metal hex-head screws and washers then had them chromed. I used these to replace the screws that came with the flares. I think it looks a lot better than the plastic buttons.

Yeah, thats what I got. Cheaper price, still quality product. Those boot thing the OP is talking about, they come with the flares. I, myself, never put them on, but They ae here in the box still. And yes, you drill holes into the jeep, but Ity is pretty easy and looks 1000 times better.

You can actually find these on EBay with or without the "boot" you mention. I put them on with my flares because there are 2 holes in the body after you remove the stock ones. I also like the idea that I can replace a flare if I damage one without having to buy a whole new set.